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- PDB-5c2y: Crystal structure of the Saccharomyces cerevisiae Rtr1 (regulator... -

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Basic information

Entry
Database: PDB / ID: 5c2y
TitleCrystal structure of the Saccharomyces cerevisiae Rtr1 (regulator of transcription)
ComponentsRNA polymerase II subunit B1 CTD phosphatase RTR1
KeywordsHYDROLASE / regulator of transcription / zinc finger motif / phosphatase
Function / homology
Function and homology information


: / RNA polymerase II CTD heptapeptide repeat phosphatase activity / RNA polymerase core enzyme binding / RNA polymerase II transcribes snRNA genes / protein-serine/threonine phosphatase / transcription by RNA polymerase II / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Rtr1/RPAP2 domain / Rtr1/RPAP2 domain / Rtr1/RPAP2 domain superfamily / Rtr1/RPAP2 / Rtr1/RPAP2 family / RTR1-type zinc finger. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
RNA polymerase II subunit B1 CTD phosphatase RTR1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsYogesha, S.D. / Irani, S. / Zhang, Y.J.
CitationJournal: Sci.Signal. / Year: 2016
Title: Structure of Saccharomyces cerevisiae Rtr1 reveals an active site for an atypical phosphatase.
Authors: Irani, S. / Yogesha, S.D. / Mayfield, J. / Zhang, M. / Zhang, Y. / Matthews, W.L. / Nie, G. / Prescott, N.A. / Zhang, Y.J.
History
DepositionJun 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA polymerase II subunit B1 CTD phosphatase RTR1
B: RNA polymerase II subunit B1 CTD phosphatase RTR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9858
Polymers42,4742
Non-polymers5116
Water32418
1
A: RNA polymerase II subunit B1 CTD phosphatase RTR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5875
Polymers21,2371
Non-polymers3504
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA polymerase II subunit B1 CTD phosphatase RTR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3993
Polymers21,2371
Non-polymers1612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-43 kcal/mol
Surface area17910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.009, 119.009, 69.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein RNA polymerase II subunit B1 CTD phosphatase RTR1 / / RNA polymerase II-associated protein 2 homolog RTR1 / Regulator of transcription 1


Mass: 21237.148 Da / Num. of mol.: 2 / Fragment: UNP residues 1-178
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RTR1, YER139C
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P40084, protein-serine/threonine phosphatase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.5 % / Description: needle shape
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES pH 7.5, 1.25M Lithium sulfate / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.288 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 15, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.288 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 14886 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rsym value: 0.169 / Net I/σ(I): 9.24
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.32 / % possible all: 71.2

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.6→45.181 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2624 1486 9.99 %Random selection
Rwork0.2066 ---
obs0.2123 14868 93.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→45.181 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2845 0 23 18 2886
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092922
X-RAY DIFFRACTIONf_angle_d1.2123932
X-RAY DIFFRACTIONf_dihedral_angle_d16.2231117
X-RAY DIFFRACTIONf_chiral_restr0.043421
X-RAY DIFFRACTIONf_plane_restr0.006509
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5994-2.68330.38231050.31948X-RAY DIFFRACTION75
2.6833-2.77920.37141260.29921131X-RAY DIFFRACTION89
2.7792-2.89050.39981360.27821221X-RAY DIFFRACTION96
2.8905-3.0220.32191380.27811244X-RAY DIFFRACTION98
3.022-3.18130.3081390.2691247X-RAY DIFFRACTION98
3.1813-3.38060.2911400.23011267X-RAY DIFFRACTION98
3.3806-3.64150.26211410.19561265X-RAY DIFFRACTION97
3.6415-4.00770.21811380.17491246X-RAY DIFFRACTION97
4.0077-4.58720.20711400.15581262X-RAY DIFFRACTION96
4.5872-5.77740.22681400.16161259X-RAY DIFFRACTION95
5.7774-45.18820.21371430.17711292X-RAY DIFFRACTION91

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